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Nucleic Acids Research Advance Access published online on October 22, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp875
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Ron Caspi1, Tomer Altman1, Joseph M. Dale1, Kate Dreher2, Carol A. Fulcher1, Fred Gilham1, Pallavi Kaipa1, Athikkattuvalasu S. Karthikeyan2, Anamika Kothari1, Markus Krummenacker1, Mario Latendresse1, Lukas A. Mueller3, Suzanne Paley1, Liviu Popescu1, Anuradha Pujar3, Alexander G. Shearer1, Peifen Zhang2 and Peter D. Karp1,*

1SRI International, 333 Ravenswood, Menlo Park, CA 94025, 2Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305 and 3Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA

*To whom correspondence should be addressed. Tel: +1 650 859 4358; Fax: +1 650 859 3735; Email: pkarp{at}ai.sri.com

Received September 30, 2009. Accepted October 1, 2009.

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism.


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